Research workbench
Mouse TRPM8 in lipid nanodiscs in the presence of calcium and icilin
Analyse Mouse TRPM8 in lipid nanodiscs in the presence of calcium and icilin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7WRE
- Type
- protein
- Length
- 3,720 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transient receptor potential cation channel subfamily M member 8
- UniProt
- Q8R4D5
- Ligands
- KX7, CA
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · 1 distinct chain · 62% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Transient receptor potential cation channel subfamily M member 8 | protein | 930 | 62% helix, 5% strand | Q8R4D5 |
Ligands and binding sites
- KX7 · Icilin · ligand · 4 copies · chains A, B, C, D
- CA · Calcium ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 506 | 0.83 | 0.90 | 35 | empty |
| 2 | 959 | 0.79 | 0.81 | 81 | KX7 |
| 3 | 956 | 0.79 | 0.81 | 77 | CA, KX7 |
| 4 | 894 | 0.79 | 0.81 | 66 | CA, KX7 |
| 5 | 975 | 0.79 | 0.80 | 74 | KX7 |
Interfaces
6 interfaces between chains.
- A–D · 3964 Ų buried · 29 hydrogen bonds · protein-protein
- A–B · 3962 Ų buried · 29 hydrogen bonds · protein-protein
- B–C · 3952 Ų buried · 29 hydrogen bonds · protein-protein
- C–D · 3950 Ų buried · 29 hydrogen bonds · protein-protein
- A–C · 49 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 7WRE · Mouse TRPM8 in lipid nanodiscs in the presence of calcium and icilin · the same entry in another collection · chain A against A, TM-score 1.00
- Q8R4D5 · AlphaFold monomer V2.0 prediction for transient receptor potential cation channel… · a predicted model of the same protein · chain A against A, TM-score 0.89
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt Q8R4D5
- Elsewhere: RCSB PDB 7WRE · PDBe 7WRE · UniProt Q8R4D5
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